rs10508313

Variant names:

• chr10-6791131-C-T
• rs10508313
• ENST00000436383.3:n.538+9645C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436383.3(LINP1):​n.538+9645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,076 control chromosomes in the GnomAD database, including 41,189 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (41189 hom., cov: 31)
• Consequence: LINP1 ENST00000436383.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 2 publications found

Genes affected

LINP1 (HGNC:53170): (lncRNA in non-homologous end joining pathway 1)

LINC00707 (HGNC:44691): (long intergenic non-protein coding RNA 707)

ENSG00000307964 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00707	NR_038291.1	n.473+9645C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINP1	ENST00000436383.3	n.538+9645C>T		intron_variant	Intron 2 of 4	2
LINP1	ENST00000648093.1	n.522+9645C>T		intron_variant	Intron 2 of 6
LINP1	ENST00000648398.1	n.483+9645C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109206 AN: 151958 Hom.: 41165 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.740

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.719 AC: 109271 AN: 152076 Hom.: 41189 Cov.: 31 AF XY: 0.720 AC XY: 53554 AN XY: 74368

African (AFR) AF: 0.493 AC: 20441 AN: 41434

American (AMR) AF: 0.779 AC: 11894 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2682 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3022 AN: 5152

South Asian (SAS) AF: 0.585 AC: 2820 AN: 4820

European-Finnish (FIN) AF: 0.921 AC: 9775 AN: 10610

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56084 AN: 67998

Other (OTH) AF: 0.742 AC: 1567 AN: 2112

Alfa AF: 0.788 Hom.: 28120

Bravo AF: 0.700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10508313; hg19: chr10-6833093;